Probing Supra-tc Conformational Exchange in proteins: Insight into Molecular Recognition
Internal motions with diverse timescale (ps–ms) play a crucial role to govern protein function. Molecular recognition events are strongly influenced by motions between the globular rotational correlation time (τc ~ 4 ns) and 40 µs1, known as supra-τc window.2 This previously hidden timescale window came into evidence from RDC-enhanced structural ensembles of Ubiquitin.2 I will present how we have extended the kinetic limit of detection to 2.5 µs by using high power spin-lock in R1ρ relaxation dispersion (RD) experiments, which enabled us to detect the supra-τc motion directly and precisely. These experiments showed that side chains of both ubiquitin and the third immunoglobulin binding domain of protein G (gb3) move on the µs timescale through redistribution of the populations of their side-chain rotamers, which interconvert on the ps to ns timescale, making it likely that this “population shuffling” process is a general mechanism.3
The high spin-lock power R1ρ RD experiments also facilitated the detection of supra-τc motion for the first time in the backbone of GB3 protein, which is routinely being studied by NMR spectroscopists for several years. Backbone dynamics at various temperatures between 262 K and 275 K, in super-cooled conditions, revealed the existence of a global motion in the first β-turn (G9–K13) region of GB3. Lower supra-τc order parameters and enhanced fluctuations in the RDC ensemble also indicate the plasticity of the first β-turn region to one-digit microsecond timescale motion.
Interestingly, the same region of the protein takes part in binding during antibody recognition. Energy landscape, obtained via Eyring relationship between the exchange rate and temperature, indicates that the conformational exchange in GB3 involves multiple conformers within ground state.
1. Michielssens, S.; Peters, J. H.; Ban, D.; Pratihar, S.; Seeliger, D.; Sharma, M.; Giller, K.; Sabo, T. M.;
Becker, S.; Lee, D.; Griesinger, C.; de Groot, B. L., A designed conformational shift to control protein
binding specificity. Angewandte Chemie 2014, 53 (39), 10367-71.
2. Lange, O. F.; Lakomek, N. A.; Fares, C.; Schroder, G. F.; Walter, K. F.; Becker, S.; Meiler,
J.; Grubmuller, H.; Griesinger, C.; de Groot, B. L., Recognition dynamics up to microseconds
revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008, 320 (5882), 1471-5.
3. Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Schwiegk, C.; de Groot, B. L.; Becker, S.; Griesinger, C.;
Lee, D., Population shuffling of protein conformations. Angewandte Chemie 2015, 54 (1), 207-10.
Investigation of Neutral and Cationic States of the N-H...X Hydrogen Bond
Synthesis and Application of KCC-1 Supported Ultra-Small Metal Nanocatalysts
Regulation of all-trans-lycopene in Photosynthetic Organisms: Role of Light and Redox Equivalents
Optical Sensors for Detecting Metal Ions and PH Changes in vivo
Nanostructured Silica-Titania Hybrid Material using Fibrous Nano-Silica (KCC-1) as Hard Template for Photocatalysis
Light-matter strong coupling: a molecular perspective
Light-matter interactions have been extensively studied by physicist in quantum optics and condensed matter physics,  but there are only fewer attempts to understand this effect in molecular science. [2, 3] Here, we are trying to understand the hybridization of photons with organic and semiconductor molecules in a confined electromagnetic field created by Fabry-Perot cavities or plasmonic nanostructures. Our studies clearly show that both the physical and chemical properties of such systems can be changed drastically. For example, chemical reaction rates, thermodynamics, work function, phase transition and conductivity etc. of molecular systems are affected upon strong coupling. [4-7] First part of the presentation mainly covers different aspects of electronic strong coupling (ESC) and later about our recent developments on ground state vibrational strong coupling (VSC) and its impact on modifying molecular properties. [8, 9] Last part of the presentation discusses the future perspective of this new emerging area of physical chemistry.
 Haroche, S.; Kleppner, D.,Phys. Today 1989, 42, 1;  Pockrand, I.; Brillante, A.; Möbius, D., J. Chem. Phys. 1982, 77, 6289;  Lidzey, D. G.; Bradley, D. D. C.; Skolnick, M. S.; Virgili, T.; Walker, S.; Whittaker, D. M., Nature 1998, 395,53;  Hutchison, J. A.; Schwartz, T.; Genet, C.; Devaux, E.; Ebbesen, T. W., Angew. Chem. Int. Ed. 2012, 51, 1592 ;  Wang, S.; Mika, A.; Hutchison, J. A.; Genet, C.; Jouaiti, A.; Hosseini, M. W.; Ebbesen, T. W., nanoscale 2014, 6, 7243 ;  Hutchison, J. A.; Liscio, A.; Schwartz, T.; Canaguier-Durand, A.; Genet, C.; Samori, P.; Ebbesen, T. W., Adv. Mater. 2013, 25, 2481;  Orgiu, E.; George, J.; Hutchison, J. A.; Devaux, E.; Dayen, J-F.; Doudin, B.; Stellacci, F.; Genet, C.; Samori, P.; Ebbesen, T. W., Nat. Mater. 2015, 14, 1123-1129;  Shalabney, A.; George, J.; Hutchison, J.A.; Pupillo, G.; Genet, C.; Ebbesen, T.W., Nat. Commun. 2015, 6, 5981;  George, J.; Shalabney, A.; Hutchison, J. A.; Genet, C.; Ebbesen, T. W., J. Phys. Chem. Lett. 2015, 6, 1027-1031.
New experimental and theoretical approaches for determining conformation of amyloids
Chiral plasmon coupling and light-matter strong coupling
Circular dichroism (CD), an important property of chiral molecules, is extensively employed to understand the structure and conformational changes of biomolecules. Here we were trying to mimic biological evolution of chirality through bio-mineralization and successfully created metal nanoparticles with interesting chiroptical properties. Chirality transfer from chiral organic and biomoleules to metal nanoparticles has been studied and we could generalize the concept of Surface Plasmon coupled Circular Dichroism (SP-CD) in chiral nanoparticle systems which is similar to a phenomenon observed in molecular and biological system called Exciton Coupled Circular Dichroism (EC-CD). Later part of presentation discusses about the discrimination in energy transfer with chiral nanomaterials through energy transfer and laser trapping crystallization techniques.
Second part of the presentation will be a general introduction to strong molecule-molecule and light-molecule interactions. Here, we are trying to compare Kasha’s exciton coupling model to light-molecule strong coupling processes. The presentation finishes with the highlights of our recent research on improving molecular and material properties.[3, 4]
 George, J.; Thomas, K. G.,J. Am. Chem. Soc. 2010,132, 2502-2503;  Yuyama, K.; George, J.; Thomas, K. G.; Sugiyama, T.; Masuhara, H., Cryst.Growth Des. 2015 (in press);  Orgiu, E.; George, J.; Hutchison, J. A.; Devaux, E.; Dayen, J-F.; Doudin, B.; Stellacci, F.; Genet, C.; Samori, P.; Ebbesen, T. W., Nat. Mater. 2015, 14, 1123-1129;  George J.; Wang, S.; Chervy, T.; Canaguier-Durand, A.; Schaeffer, G; Lehn, J-M.; Hutchison, J. A.; Genet, C.; Ebbesen, T. W. Faraday Discuss. 2015, 178, 281-294.
Ultrafast Infra-red Spectroscopy as a Probe of Chemical Reaction Mechanisms
The timescales for reactions in solution are very fast, with lifetimes of reactive or energized intermediates that can be as short as a few picoseconds. Nevertheless, these intermediates can be observed, and the flow of energy released by exothermic reactions can be followed using techniques based on ultrafast infra-red spectroscopy. Two-dimensional infra-red spectroscopy (2DIR) provides further insights into structural changes and energy flow in molecules on these very short timescales. This talk will introduce the techniques of ultrafast time resolved infra-red and 2DIR spectroscopy and illustrate their application to the study of the mechanisms of chemical reactions. Examples will be drawn from our work on radical reactions in solution, photochemistry of hydrogen-bonded DNA base pairs, and vibrational dynamics in transition metal complexes.
Synthetic Molecules and Materials as Models of the Oxygen Evolving Complex of Photosystem II
Efficient catalytic water oxidation is an important reaction for the development of solar hydrogen as a source of green energy. Extraction of high energy electrons from water for the preparation of fuel leaves O2 as a byproduct. Nature boasts the only truly effective catalyst for this reaction, the oxygen evolving complex (OEC), a tetramanganese-calcium-oxo cluster. Though decades of research has gone to the synthesis of biologically-inspired Mn-O clusters, these systems fall short in biomimetic reactivity in comparison to other metal systems (Ru, Co, Ni, and Cu for example), which begs the question: Why have we been unable to mimic the biological chemistry with manganese?
Geometric rearrangements, and changes in coordination number are known to occur in the OEC, but current model chemistry relies heavily on chelation to stabilize synthetic clusters, rendering them inert, and without open coordination sites. Our group at Temple is exploring a new approach to manganese cluster synthesis, using sterics of bridging and terminal ligands to direct sterics and coordination number. Through our approach, we are able to access biologically relevant geometries, and prepare unchelated clusters with significant reactivity seen rarely (or never) in decades of chelate clusters. These reactivities include N-N and C-N bond cleavage, hydrogen atom transfer, ligand exchange, reductive elimination, and cluster rearrangement.
A second topic is the exploration of solid-state layered manganese oxides (termed birnessite) in the chemical and electrochemical oxidation of water. The birnessite phase of MnO2 is typically viewed as a poor water oxidation catalyst, but modification of the material by the introduction of highly active “defect” sites turns this material from a poor catalyst into an active catalyst for water oxidation. The studies being undertaken may shed light on the identity and structure of these sites and aid the development of rubust and affordable catalysts for this important reaction.
Ultrafast Vibrational Sum-Frequency Spectroscopy and Dynamics at Mineral/Aqueous Interfaces
The properties of water at interfaces are important in many disciplines. However, it is not clear what effects the presence of the surface, the charge that can develop on the surface, the solution ionic strength, and the interfacial electric field, have on how interfacial water molecules communicate with each other, e.g., how thermal (vibrational) energy flows. To address these issues we investigated the ultrafast vibrational population and dephasing dynamics of the O-H stretch using IR pump-vibrational Sum Frequency Generation (vSFG) probe at the water/mineral interfaces. Contrary to previous reports, the vibrational lifetime of the O-H stretch at the silica/water interface is ~ 600 fs, a factor 2-3 slower than bulk water, when the surface is neutral. Charging the SiO 2 interface appears to lead to a dramatic acceleration of vibrational relaxation. Experiments on the effect of ionic strength, suggest that the primary reason for accelerated dynamics at pH=6
is the sampling of water within the Debye length that has bulk-like solvation. The pH dependent structuring of interfacial water and the influence of electrolyte also impact interfacial reactivity.
A newly developed SFG spectrometer, based on a novel ultrabroadband optical parametric amplifier generating IR pulses in the ~2800-6000 cm -1 range bandwidths >2000 cm -1 in the near-IR range, allows vSFG spectroscopy, including low-intensity features such as non-hydrogen bonded OH vibrations and combination [stretch+bend] and overtone bands of interfacial water. Access to these modes opens up opportunities for investigations of a broad range of interfaces.
- The Effect of Electric Fields on the Ultrafast Vibrational Relaxation of Water at a Charged Solid-LiquidInterface as Probed by Vibrational Sum Frequency Generation, A. Eftekhari-Bafrooei and E. Borguet, J.Phys. Chem. Lett.,, 2, 1353-1358 (2011)
- Experimental Correlation Between Interfacial Water Structure and Mineral Reactivity. Dewan, S.;Yeganeh, M. S.; Borguet, E., J. Phys. Chem. Lett., 2013, 4 (11), 1977-1982.
- Observation of the Bending Mode of Interfacial Water at Silica Surfaces by Near Infrared VibrationalSum-Frequency Generation Spectroscopy of the [stretch+bend] Combination Bands. Oleksandr Isaienko, Satoshi Nihonyanagi, Devika Sil, and Eric Borguet, J. Phys. Chem. Lett., 4, 531-535, (2013)
Playing dice withzeolite secondary building blocks
Our laboratory has been using an organic soluble phosphate monoester (ArO)P(O)(OH) (Ar = 2,6-diisopropylphenyl) as the primary building unit (PBU) to assemble a large number of polyhedral molecules that resemble one or more of zeolite secondary building units and display various functions.1-4 While the reaction of this phosphate with a divalent metal ion (e.g. Zn2+) in a donor solvent predominantly leads to the isolation of stable tetranuclear metal phosphates [(ArO)PO3Zn(L)]4 which possess a Zn4O12P4 D4R SBU inorganic core. In recent times, however, we have unraveled that it is possible to also isolate other SBUs, starting from the same set of reactants, but by making small variations in the reaction conditions. Now it is possible to isolate hitherto unknown discrete D6R and D8R SBUs (which possessZn6O18P6 and Zn8O24P8cores, respectively) by switching the solvent from methanol to acetonitrile and the co-ligand from DMSO to either 4-formylpyridine5 or 4-cyanopyridine.6From a series of experimental observations it has now become apparent that, irrespective of the conditions employed, S4R SBUs are formed as the initial products. It is quite intuitive to conclude that a face-to-face fusion of two S4R blocks will lead to the formation of a D4R SBU. The explanation for the formation of larger SBUs such as D6R and D8R from a S4R however would need a different two-stage mechanism involving (a) side-by-side fusion of two or more S4Rsand (b) a constructive folding to close up the double-n-ring (n = 4, 6, or 8) SBUs. One cannot discount the possibility of misfolding in step (b), which will lead to the isolation of polymeric chains with a staircase conformation. Similarly, formation of larger S6R and S8R SBUs in the initial phase of the reaction cannot also be ignored. A rationalization of these building principles will be presented in this lecture.
1. Kalita, A.C.; Roch-Marchal, C.;Murugavel, R.Dalton Trans., 2013, 26, 9755.
2. Kalita, A.C.; Murugavel, R.Inorg. Chem., 2014, 53, 3345.
3. Kalita, A.C.; Gogoi, N.;Jangir, R.; Kupuswamy, S.; Walawalkar, M. G.; Murugavel, R.Inorg. Chem.,2014, 53, 8959.
4. Kalita, A.C.; Sharma, K.; Murugavel, R. Cryst. Eng. Comm.2014, 16, 51.
5. Gupta, S.K.; Dar, A. A.; Rajeshkumar, T.; Kuppuswamy, S.; Langley, S. K.; Murray, K. S.; Rajaraman, G.; Murugavel, R. Dalton Trans. 2015, 44, 5587.
6. Gupta, S.K.; Kuppuswamy, S.; Walsh, J. P. S.; McInnes, E. J. L.; Murugavel, R. Dalton Trans. 2015, 44, 5961.
7. Gupta, S.K.; Kalita, A.C.; Murugavel, R. unpublished
8. Dar, A.; Murugavel, R. unpublished
9. Dar, A.; Sharma, S. K.; Murugavel, R. Inorg. Chem. 2015,54, 7953.
10. Dar, A.; Gupta, S. K.; Sen. S.; Patwari, G. N.; Murugavel, R. Inorg. Chem. 2015,54, 0000.
EPR and the Binding of Molecules to Cytochrome P450 Enzymes
The cytochromes P450 are a large enzymes superfamily found in every branch of life. Some isoforms help synthesize essential compounds and are attractive targets for antibiotics. Other isoforms metabolize many pharmaceutical drugs and are one source of drug interactions. Many drugs directly bind heme in the active site but our pulsed EPR studies show a new binding mode with a water as a bridge between heme and drug, sometimes retaining enzymatic activity
Seeing enzymes in action
Single-molecule studies of electron-transfer between copper centers of small laccase (SLAC) from S. coelicolor
Single molecule enzymology provides an unprecedented level of detail about aspects of enzyme mechanisms which have been difficult to probe in bulk. One such aspect is intramolecular electron transfer (ET) which is a recurring theme in the research on oxidoreductases. Recently, we introduced a technique to study ET in enzymes at single molecule level by means of confocal fluorescence microscopy (PNAS. 2008, 105, 3250).
I will present recent results on an enzyme, small laccase (SLAC), from S. coelicolor which converts O2 to H2O with concomitant oxidation of organic substrate(s). SLAC is unique, among commonly studied multicopper oxidases (MCO), in its structure (being a homo-trimer of two-domain monomers) and function where it employs a so-called type 1 (T1) Cu site, a trinuclear Cu centre (TNC) and a tyrosine residue (Y108) to catalyze this process which has a high activation barrier. I have measured, for the first time, intramolecular ET rates between the T1 and TNC of SLAC during turnover, one molecule at a time. The distribution across many molecules shows an average ET rate ~450 s-1 independent of substrate concentration, consistent with the proposed enzyme mechanism and with the results of transient kinetics experiments. The activation energy for ET amounts to 350 meV and varies from molecule to molecule with a spread of ±25 meV. Experiments are underway to measure other microscopic rate constants in the enzymatic cycle which have never been measured in bulk. The method is suitable to study ET in a wide range of redox active enzymes in-vitro as well as in-vivo.